Undiscovered Secrets
by jmingle8
Summary: On the night of The Snowmen, what if Clara never died? Would the Doctor find out who she really is? Would he reach Trenzalore? Would they discover his greatest secret? AU
1. Chapter 1

Clara shrieked as she was pulled out the TARDIS and plummeted to some impending doom. She landed with a thud, and lay there, restless, broken, and unconscious.

The Doctor quickly whipped the TARDIS off its cloud and materialized it in front of the Victorian manor. "How could I have lost another one, a friend, a curious civilian, on the first day?" he thought to himself. Still recovering from losing the Ponds, he had secluded himself from the world, parked the TARDIS on a cloud in Victorian London, and had determined to stay away from anyone except, on occasion, Jenny, Vastra, and Strax. He had struggled to block out most of his memories, especially the most recent. However, as of late, some of them momentarily came back to him, which forced him to relive them, and give him another reason to be alone. Yet he found himself drawn to Clara, as she was what brought him out of "retirement". However, the outcome only reminded him of why he stopped being he savior of Earth, because it always ended dead with someone dead. What would become of him?

The Doctor quickly materialized the TARDIS around her, and immediately moved the TARDIS again to inside the house. He grabbed her, held her tight, carried her to the door, and placed her gently onto the table. Immediately, she was surrounded by Jenny, Vastra, Strax, and the Latimer family. He politely pushed them out of the way, and whipped out his always-handy sonic screwdriver. The whirring noise of the screwdriver and the steady green light made him more hopeful for good news then ever. As he moved the piece of equipment across her body, it scanned her vitals and came back with a diagnosis. "Concussion, Internal Bleeding, and Broken Leg" it read. The Doctor swiftly turned to face Strax. "Watch her," he pleaded. "Don't let her out of your sight, and if she awakes, tell her to keep her head down and fetch her a glass of water."

"Roger that, sir. And if I may ask, where shall you be going?"

"To finish this, once and for all."

"May I suggest bringing a grenade?" Strax asked as he leaned slightly over to the Doctor.

"Why not."

Strax finished, "I suggest bringing a grenade."

Before Strax could finish his sentence, the Doctor whisked around the corner and into the TARDIS, and it disappeared into thin air, going only he knows where. He went to Dr. Simeon's office, to defeat the Great Intelligence. Meanwhile, the Latimer family thought they lost their nanny. The kids cried more severely than anyone. Jenny tried to console them, but to no avail.

The Doctor now had a cause to defeat the Great Intelligence, to avenge Clara. He quickly maneuvered the TARDIS inside the Great Intelligence office.

"Hand me the box, Doctor!" screamed Dr. Simeon. The Doctor reluctantly gave it to him.

As Dr. Simeon opened it, the Doctor replied, "Are you sure you want to do that?" Dr. Simeon disregarded this warning, and opened the box that contained fragments of the frozen ice governess. To his surprise, he was bitten by a memory worm, which successfully drained decades of memories with the Great Intelligence from his brain. The Doctor expected the Great Intelligence to be defeated on the spot due to Dr. Simeon's lack of memory. However, it cackled maniacally at the Doctor.

"You thought you could defeat me?" the Great Intelligence retorted. "You thought it would be easy?" The Doctor was visibly confused. During his moment of confusion, the snow suddenly turned to water, and the snow outside turned to rain.

"Of course!" he said dumbfoundedly. "The one thing that change the snow to rain. The only emotion more powerful than hate. Love. A whole family crying on Christmas Eve is enough to drown out the signals."

At this realization, he hopped back into the TARDIS and, before long, he returned to the Latimer mansion. Greeted by a semi-conscious and visibly wounded Clara, the Doctor grabbed her hand, sat gently beside her, and said, "You did it. You saved the world." He was exaggerating a bit, but a dying woman wasn't looking for the truth.

"Run you clever boy, and remember," she breathlessly forced out of her mouth. The Doctor's expression changed. He'd heard that before, but couldn't remember where.

She closed her eyes, as if for the last time, and breathed perhaps last breath. Her chest sunk, and the Doctor panicked. He paced around the room, trying to hold in his tears unlike the rest of the room, and mindlessly thought about his carelessness in letting someone else die. Meanwhile, Captain Latimer, Alice, and the children wept and wept until they cried themselves dry. Their mysterious governess had left them, her secret voice, her name, and her life were all gone.

The only person still focused on her was Strax, who denied the notion the she was dead, and tried as much as he could to bring her back to life.

"Strax," the Doctor called. "What are you doing?"

"Bringing Clara back to life, sir."

"With what, may I ask."

"Top-secret Sontaran nursing equipment. If any human eyes look at it, they burn up." Strax looked at the Doctor, specifically his eyes. "Sir, your eyes. They're not burning."

"I'm not human." The Doctor replied matter-of-factly. Strax went back to work, and the Doctor went to console the family.

Just as the gloominess of the room seemed to have no end, a beep surfaced from Strax's machine. Clara's stomach rose, her nostrils flared, and her eyes partially widened. To the surprise of everyone, she had survived. With all odds against her, she awoke to the aghast faces of the room and a general panic to keep her awake at all costs. In the end, she triumphantly sat up and took a sip of water. At the reluctance of their father, Francesca and Digby stayed at Clara's bedside all night. It even bothered Clara at times. "Oi, could you be any louder? You'll wake up the whole house!" Clara quietly exclaimed to Digby.

"Sorry," Digby replied.

After a moment of silence, Digby asked Clara, "So who are you? Are you Clara, Ms. Montague, or both? Are you really who you say you are?" Clara was surprised at his question. She didn't know how or with what to respond.

"Let's just say that there is a lot you don't know about me," she eventually responded to the children. "Now go to bed." They hustled across the room and scuttled up the stairs.

Waiting for the perfect moment, the Doctor popped his head out the TARDIS and saw that Clara was alone. He casually walked out to check on her. "Doctor, is that you?" she asked the figure that moved toward her side.

"Yes, how are you doing?"

"Fine. So when are we leaving?" Clara croaked out in a hoarse, tired voice. The Doctor's shock could be seen in his face. Why would she want to leave at all, let alone soon?

"Not now." She needed bed rest. They both knew it. The Doctor walked over to her, kissed her gently on the forehead, and went back into the TARDIS. It evaporated into thin air before Clara's eyes, before they shut themselves as she fell asleep.

Clara had a little while to wait before she would be ready for the Doctor's adventures. However, the Doctor had a time machine in his hands, and he didn't have to wait more than a minute. Clara, still lying in bed, was eating breakfast seven days after her death-defying fall. The TARDIS materialized ten feet away, and the Doctor kicked open the door. He was immediately greeted by Clara's question again.

"Are we leaving now?" At this question, the Doctor grabbed Strax's machine and checked on her health. She was perfectly fine, and didn't even have a scratch. At this response, Clara jumped out of bed and strolled over to the TARDIS, opened the door, and was re-mesmerized. The shiny knobs and handles, the sheer size of the machine, and presence of the Doctor all at once almost made her pass out again. The Doctor rushed to the console, grabbed a handle, and shut the door.

"Is it always this dangerous?" Clara asked, visibly shaken.

"Yes," the Doctor replied. "Why, does that make you change your mind?"

"No, that's what makes it better." She whipped her head around to check the door for any frozen ice governesses. She turned back and said, "Sorry, force of habit." The Doctor cracked a smile. It quickly diminished, as he remembered what she had said before. Still unable to recall where he had heard it before, he realized that he should mention it to her.

"What you said before. Your 'last' words. I've heard them before. Where? Do I know you?" Clara was wordless. She didn't know what to say. Of course she'd never met him before, she would've remembered. "You're keeping secrets from me," he stated as he anxiously awaited her reply.

"Who doesn't? I know you are keeping more than a few." The Doctor couldn't let this go. She was a mystery waiting to be solved. A puzzle waiting to be pieced together. A girl waiting to be discovered. The impossible girl. Yet, he didn't know what was "impossible" about her. Something was weird about her. Something was familiar about her. He had finally found someone to fill the void in both his hearts, but she was a mystery, which is why he liked her. The Doctor swiftly faced her and, after months of loneliness, asked her as the TARDIS disappeared and flew into the time vortex, "Where do you want to go?" He had finally found her. He finally found his companion.


	2. Chapter 2

Clara peeked outside her window. Underneath the aging tree in the front yard sat the TARDIS, as deep a blue as always. She was finally used to the old blue box, yet traveling with the Doctor was still foreign to her. Every week, she waited with anticipation for Saturday, the day when she didn't know where she was going or what she was doing. All she knew was that she was going to see something remarkable. That day had come again, and she had prepared as she always did: by sitting and waiting.

The Doctor constantly had another place to go; another thing to see. He could take Clara to every possible place that could be visited, and still have more to show her. And while Clara had to patiently count down the days to see him again, the Doctor could just push a few buttons, pull a few levers, and, within seconds, go on another adventure with her.

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The Doctor anxiously paced through the TARDIS' hallways. Pretty soon, Clara would waltz in through the police box doors and travel with him through time and space. Even though he didn't have to wait as long as Clara for their adventures, he still got tired of waiting, even if he only waited a few minutes. Being a time traveler, he gradually lost his patience, but he also learned that everything comes to an end eventually, so he needs to spend his time wisely, as someone or something could be gone at any moment. This is why he enjoyed spending time with Clara. However, every minute spent with her meant another minute closer to learning who she was. She may not know that she is special, but the Doctor did. He knew that something made her different. Something connected them in a way that neither of them knew. But time was running out for the Doctor, and, with only a little time left, he would do anything to learn what it was.

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Clara snuck outside in the hope that she wouldn't be seen by the Latimers, as they didn't know she went traveling with the Doctor every Saturday, as she seemingly returned to them the same second she left. She knocked three times on the TARDIS door, and it opened before her. Dashing across the lawn, running for the blue box, she strolled in and was greeted by the Doctor as he skipped down the steps and ran to the console, a bright smile on his face. "Where are you taking me today?" Clara asked. There were millions of possible answers, but the Doctor had only one in mind. He raced around the console, threw a few levers, the TARDIS lurched and jumped and, before her eyes, Clara was brought to a new planet.

"Come see for yourself," the Doctor replied. They both exited the police box, and the Doctor turned to Clara. She was visibly mesmerized by what was in front of her, a billowing waterfall surrounded by luscious plants. Specifically, there was an abundance of roses. The water sprayed onto them, and their petals glistened with it. To the left of the TARDIS was a large tropical rainforest that beckoned for the Doctor and Clara's attention with its exotic colors and strange noises. To the right, however, was a collection of gardens that were overflowing with roses of all colors. Before Clara could ask, the Doctor said, "Welcome to Terrosa, or as it's locally known, the Planet of Roses. Known for its flowers, it is a popular destination for, well, couples." The Doctor looked aside and avoided eye contact with Clara. He began to blush and hoped she hadn't heard what he said. Clara grinned and looked up at the Doctor.

"So does that make us a couple? Are you leading me on?" She batted her eyelashes and excitedly awaited a reply. The Doctor attempted to recover from his flustered state and cleared his throat.

"No, I just thought... Maybe you'd enjoy... Pretty... Shut up." Clara snorted and elbowed him in the stomach, causing him to step back and look down at her. He stammered, "Don't- Don't- Don't do that." Clara looked back at the skyline.

"Well, it is pretty." At this, they made their way to the right, keen to explore, and headed toward the garden of roses.

There were less roses than expected in the gardens, but there were still plenty to see. Over 100 mini gardens were contained in little greenhouses, each containing two rows of ten roses. It all looked very quaint and picturesque. Together, they kept walking until they reached one random garden, and randomly entered, hoping it would lead to them to something interesting. When they entered, they noticed a faint, scream-like noise, and while it would be perceived as nothing to most, both the Doctor and Clara were able to make it out. "Doctor, what's that noise? It sounds like someone's shrieking. Oi, it's getting on my nerves," she said as she clasped her ears with her hands.

"Don't know," the Doctor calmly answered. "It's probably nothing." But he knew otherwise, as it was always something, and it was usually a joy for him to try and figure it out. He reached inside his jacket pocket, and grabbed his sonic screwdriver. After briefly scanning the area, it beeped as it detected that the sound was coming from the roses. "What do you know, it's the roses!" The Doctor exclaimed. Clara was as surprised as the Doctor.

"But it sounds like human voices. How can it be coming from a rose?" Clara questioned the results. "We should check another garden," Clara suggested. The Doctor agreed with her.

They walked across the path between gardens and approached another entrance. The Doctor opened the door and walked in, followed closely by Clara. Immediately, Clara recognized the same noise as before. "The noise is here too. Do you think it's like this in all of the gardens?" she asked.

"Most likely," the Doctor mumbled, still studying his sonic. Wondering if she could figure it out if she examined the roses more closely, Clara picked up a rose and brought it to her face. Suddenly, the petals twisted inward and disappeared.

"Doctor!" Clara shrieked, startled by the sudden movement. The Doctor swiftly turned around, only to catch a fleeting glimpse of Clara before she too disappeared.

"Clara!" the Doctor screamed as he raced around the garden, scanning with his sonic, his mind running in circles. _Where has she gone?,_ he thought. _Was it the roses?_ After a few thundering double heart beats, his eyes widened as he came to the only possible solution. It wasn't the best idea, but it was the only one that came to mind. Without thinking any further, he picked up a rose, sniffed, amd vanished into thin air.

Clara's eyes opened, but she saw nothing. She screamed for help, but no sound came out. The rose had brought her to nowhere, a place where nothing could be seen, heard, or felt, and where nothing seemed to exist. It was a void, and Clara couldn't stand it. If she couldn't get out, it would drive her insane.

The Doctor awoke in an empty, abandoned town square. Confused, he got up and began to cautiously walk down the street. Surrounding him were old, shabby buildings that seemed to have been technologically advanced at one point, but had since become outdated. He knew he was somewhere familiar, yet he hadn't been there in a very long time. He had his suspicions as to where he was, and they were only confirmed when people walked right by him. They must not have seen him, as they walked within inches of the Doctor. The people that passed were wearing brown-red robes with golden metal headdresses that covered their shoulders and held up the back of their heads. They were wearing traditional Time Lord clothing, which meant- he was back on Gallifrey.

The Gallifreyans on the street were protesting and seemed to be searching for someone. They were putting up posters and holding signs. "_WANTED: The Doctor for crimes against the Gallifreyan empire and race" _the posters read. The Doctor was stunned, as not only were they alive, but they were looking for him- him in particular. In order to make sense of all of this, he reached into his pocket to grab his sonic screwdriver. As he did so, his hand missed and struck thin air- his sonic was missing. He patted down all of his clothes in search of his sonic screwdriver. While he looked for it, he tried to make sense of what was going on. Perhaps he was in some sort of trance, or in a suspended reality. The roses must have brought him into a personal nightmare, to a place where he never wanted to be again. Suddenly, he grabbed onto something in his other pocket. It was his sonic screwdriver. He smiled with embarrassment and thought "You didn't need the screwdriver to come to that conclusion, did you?"

Now with his sonic screwdriver in hand, he was able to confirm that the roses brought whoever touched them to a nightmare of their own making. Now, the screaming made sense. People were being trapped in a nightmare, and it was their screams that they had heard- trapped inside the roses. With a push of a button and a wave of the sonic screwdriver, the screaming from the other roses became audible. He followed the noise down the street until it was at its loudest, and pulled open a pothole in the ground that the screaming seemingly came from behind. Before him was a ladder that went deep into a pit. He followed it with his eyes, and couldn't see the end. So, he got on his knees, grabbed the top rung, and started scaling down the ladder.

Clara was in her nightmare of nothingness for what seemed like forever, but what also felt like no time at all. She knew she had to find a way out, but first she had to find what was holding her in place. Since her physical body wasn't anywhere to be seen or felt, her mind and soul was all she had to free. There was something holding her back, but there was also nothing keeping her there. This intrigued her, as did all of the time she spent in the void. Everything was all one oxymoron, and she didn't know what to do about it. Slowly, she realized that the only way to start to find a way out was to try to see something. With her mind, she pushed as much as she could, and nothing seemed to happen. She pushed harder and harder, with eventually no outcome, and then gave up. With no hope left, she just stayed there and waited in the nothing she was in.

Before long, something appeared in the corner of her eye. It was a tiny speck of light. With her mind, she reached towards it with the intention to try make it bigger. Suddenly, she could see herself and the light that seemed to be her exit. As she looked down at her arms, she noticed that she held in place by vines, vines with thorns. The roses held her in place, and the roses had brought her to this nightmare.

Now that she could see, she was able to move around. She groaned and struggled against the vines with her hands until one of them broke free. With her free hand, she undid the others for her other hand and feet. Then, she floated in mid-air, suspended in nothing. Still able to move, she drifted over to the light, propelled by her thoughts. At first glance, it seemed to be a measly few feet away. In actuality it was a few hundred feet away. When she nearly reached the exit, the light expanded and a figure popped out. "Hello!" the Doctor said cheerfully. "Clara, is that you?"

"Yes, it's me!" she responded. "How did you get here? Where or what is here?"

"Well, I got out of my nightmare by climbing down a ladder, I found a main unit, or 'Mother Rose', and shut it off, so the nightmares slowly started collapsing in on themselves and reversing," The Doctor said in a hurry. He looked around. "And just in time too. Your future would look very bad if you had been in here for much longer." Clara furrowed her brow. She was slightly disappointed that she hadn't gotten out herself, but inquisitive as to where the Doctor had been. She decided to ask later and get back to the matter at hand.

"C'mon, let's get out!" Clara shouted. They both jumped into the light, only to appear in front of the main Rose. It was just a large, functioning Rose in the center of all the nightmares. There was a tall, long stem that led up to the Rose itself. Its petals were especially thick and tall, its thorns were extra long and spiky, and the Rose itself was huge. "I thought you shut it off!"

"No, I just shut off the nightmares! We still have to get rid of the whole Mother Rose to end it for good!" At that, the Doctor grabbed onto a thorn of the jumbo sized Rose, reached out his hand for Clara, and started climbing.

Upon reaching the top, they looked at each other and thought of how to get rid of it.

"How do we get rid of it?" Clara asked.

"Well, we could do many things. We could destroy it, which seems likely, but we need to plan it first. So how do we start to destroy it?" The Doctor grabbed Clara's hand. "We jump." Before Clara could refuse, the Doctor pulled her off the edge as they began to free fall into the center of the Rose.

Clara gave the Doctor a piercing look with flaming nostrils and pursed lips. "Now what?" Clara asked upon reaching the center. Skinny and tall sticks that held pollen ran up the center of the Rose, like an actual rose. The Doctor simply ran to the petals from the inside. With his sonic screwdriver, he was able to determine the distance to the outside. They were deep inside the Rose. The only thing that blocked them from the outside was an abundance of large petals.

"The Rose's main organs and controls are in the petals. If we can break through them and destroy the wall, it should shut down the Rose and bring us back to the garden."

"But how do we break through it? I mean, the walls aren't that hard to break through, it's just that there are so many layers of the petals, making them compact." The Doctor wasn't too sure. He thought about using pure physical strength, but wondered if they would be strong enough to break through.

"We could use your arms and legs, however..." He was cut off by a loud thud. Clara had already begun work. Immediately after, so did he.

Soon, they had a large dent in the wall, but it wasn't anywhere close to the size of the hole they needed. The Doctor, however, was busy thinking of a better way to dig into the lining of the Rose. To Clara's surprise, he started climbing back up the Rose, up to the top. Clara assumed that he would dig from the outside to be more efficient, but was disproven when he returned with two rose thorns in his hand.

"What are we doing with those?" Clara asked. Instead of telling her, the Doctor tossed one to her and showed her. He began stabbing the thorn into the wall to cut into it. Surprisingly, the thorn could dig deep into the Rose's petals. At that, they continued work on the digging.

After what seemed like an hour of hard work with blood, sweat, and tears, they finally reached the end of the petals, thus destroying the controls. Then, they climbed down the stem to reach ground. Upon reaching the ground, they looked at the dilapidated rose as it began to shut down due to their triumph. When it did, the Doctor and Clara disappeared and returned to the garden. However, in the garden were 18 other people that had been trapped in the roses as well. When the Doctor took a peek out of the garden, he noticed that the people from the other gardens were starting to fill out into the main walkway. He rushed out and got everyone's attention by whistling and yelling, "Hey, enough with the confused blather! Please disregard anything that happened in your recent memory and return to wherever you came from!" The crowd was confused, but listened to the Doctor anyway.

While everyone started rushing to the exit, the Doctor and Clara stayed behind to make sure everyone left and that the planet was all in order. Before they began to walk out, they heard a crumpling noise. Upon reinspection of the gardens, all of the roses began to shrivel and die, as they had no source of life anymore. At that, the Doctor and Clara approached the TARDIS.

Before entering, Clara turned toward the Doctor and asked, "Doctor, where was I?"

"Well, you're nightmare took place in a void, but you physically were in this room, if you will. A 'virtual reality' room. It had the ability to morph into size and shape of anything you could possibly imagine. This room turned into your nightmare, as it did with me." Clara thought some more, and looked at the Doctor to ask another question.

"Doctor, what was your nightmare?" The Doctor froze. Clara had yet to learn about the Doctor's heritage and his role in the Time War, and now wasn't the best time for her to find out.

"Well, um, I was... in a cave... full of... spiders." The Doctor grinned. He didn't want Clara to think of him as being scared of spiders, but it was better than the other option.

"Look, a spider!" Clara pointed out to the Doctor as she hoped for a reaction. The Doctor played along by rushing back into the TARDIS with a playful shriek. Clara followed right behind him with a smirk on her face.

The Doctor brought her home to London. They said their goodbyes and parted ways, but only as Clara left did the Doctor take a breath and a sigh of relief. He knew that he had to savor his time with her, because one day, she wouldn't be there anymore. So the Doctor waited the full seven days before the next Saturday and their next adventure.


End file.
